INFO 2025-06-26 11:12:48,103 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2005 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 11:12:48,103 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Third unattended mission done- this one to M2. Outbound at depth, return yo-yo. - ctdToUse = ctd1 INFO 2025-06-26 11:12:48,103 process.py process_mission():449 [1] Processing AUVCTD mission 2006.088.03 by user docker_user on host eae60d30a712 INFO 2025-06-26 11:12:48,103 process.py download_process():165 [1] Download and processing steps for 2006.088.03 INFO 2025-06-26 11:12:48,103 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2006/2006088/2006.088.03 INFO 2025-06-26 11:12:48,104 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2006/2006088/2006.088.03 to /data/auv_data/dorado/missionlogs/2006.088.03 INFO 2025-06-26 11:12:54,318 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2006.088.03 INFO 2025-06-26 11:12:54,318 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.088.03/ctdDriver.log (23752387 bytes) INFO 2025-06-26 11:12:56,100 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.088.03/ctdDriver2.log (23752117 bytes) INFO 2025-06-26 11:12:57,850 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.088.03/gps.log (142772 bytes) INFO 2025-06-26 11:12:57,874 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.088.03/hydroscatlog.log (16192454 bytes) INFO 2025-06-26 11:12:59,764 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.088.03/navigation.log (79626290 bytes) INFO 2025-06-26 11:13:05,532 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.088.03/isuslog.log (1460405 bytes) INFO 2025-06-26 11:13:05,677 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.088.03/parosci.log (34687142 bytes) INFO 2025-06-26 11:13:08,456 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2006.088.03/parosci.log: [447483 691771] INFO 2025-06-26 11:13:08,540 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.088.03/tailCone.log (16200379 bytes) INFO 2025-06-26 11:13:10,505 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2006.088.03/biolume.log (18365852 bytes) INFO 2025-06-26 11:13:12,258 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 11:13:13,157 logs2netcdfs.py download_process_logs():807 [1] Time to process: 18.84 seconds WARNING 2025-06-26 11:13:13,157 process.py download_process():196 [1] No lopc.bin file for 2006.088.03 INFO 2025-06-26 11:13:13,157 process.py calibrate():227 [1] Calibration steps for 2006.088.03 INFO 2025-06-26 11:13:13,648 calibrate.py _nudge_pos():1680 [1] seg# end_sec_diff end_lon_diff end_lat_diff len(segi) seg_min u_drift (cm/s) v_drift (cm/s) start datetime of segment INFO 2025-06-26 11:13:13,650 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 11:13:14,395 calibrate.py _nudge_pos():1806 [1] 89: 0.070 0.0013592 0.0005524 6754 22.53 8.955 4.543 2006-03-29T20:25:17.253583232 INFO 2025-06-26 11:13:14,876 calibrate.py _nudge_pos():1806 [1] 136: 0.060 0.0000347 0.0000261 55 0.18 28.593 26.916 2006-03-29T20:26:14.259677824 INFO 2025-06-26 11:13:14,969 calibrate.py _nudge_pos():1806 [1] 145: 0.070 0.0014270 0.0009198 12425 41.41 5.115 4.115 2006-03-29T21:07:47.258895872 INFO 2025-06-26 11:13:15,707 calibrate.py _nudge_pos():1806 [1] 216: 0.070 -0.0003703 0.0018582 11920 39.73 -1.384 8.667 2006-03-29T21:48:41.250785792 INFO 2025-06-26 11:13:15,925 calibrate.py _nudge_pos():1806 [1] 237: 0.060 -0.0000336 -0.0000849 15 0.05 -106.816 -337.286 2006-03-29T21:49:04.259209600 INFO 2025-06-26 11:13:16,265 calibrate.py _nudge_pos():1806 [1] 268: 0.070 0.0000173 -0.0000327 20 0.06 40.563 -95.673 2006-03-29T21:49:38.256880768 INFO 2025-06-26 11:13:16,367 calibrate.py _nudge_pos():1806 [1] 278: 0.070 -0.0047060 0.0019605 11400 38.00 -18.388 9.561 2006-03-29T22:27:47.260073216 INFO 2025-06-26 11:13:16,789 calibrate.py _nudge_pos():1806 [1] 319: 0.070 -0.0000118 -0.0000151 20 0.06 -27.695 -44.161 2006-03-29T22:28:31.257059328 INFO 2025-06-26 11:13:16,889 calibrate.py _nudge_pos():1806 [1] 328: 0.070 -0.0055838 0.0015277 10210 34.03 -24.364 8.318 2006-03-29T23:02:41.256624640 INFO 2025-06-26 11:13:16,912 calibrate.py _nudge_pos():1806 [1] 330: 0.080 -0.0000109 0.0000101 15 0.05 -34.631 39.913 2006-03-29T23:02:45.256350464 INFO 2025-06-26 11:13:17,376 calibrate.py _nudge_pos():1806 [1] 375: 0.080 -0.0000057 0.0000120 15 0.05 -18.026 47.509 2006-03-29T23:03:32.253131136 INFO 2025-06-26 11:13:17,562 calibrate.py _nudge_pos():1806 [1] 393: 0.070 -0.0062232 0.0016828 9620 32.06 -28.822 9.725 2006-03-29T23:35:53.260163072 INFO 2025-06-26 11:13:17,615 calibrate.py _nudge_pos():1806 [1] 398: 0.070 -0.0000702 0.0000339 30 0.10 -107.856 65.067 2006-03-29T23:36:03.259478144 INFO 2025-06-26 11:13:17,884 calibrate.py _nudge_pos():1806 [1] 424: 0.070 -0.0000590 0.0000112 25 0.08 -109.617 25.930 2006-03-29T23:36:33.257422976 INFO 2025-06-26 11:13:17,915 calibrate.py _nudge_pos():1806 [1] 427: 0.080 0.0000178 -0.0000179 15 0.05 56.612 -70.938 2006-03-29T23:36:38.257080576 INFO 2025-06-26 11:13:18,067 calibrate.py _nudge_pos():1806 [1] 439: 0.080 -0.0000438 0.0000068 25 0.08 -81.224 15.803 2006-03-29T23:36:54.255984512 INFO 2025-06-26 11:13:18,092 calibrate.py _nudge_pos():1806 [1] 441: 0.090 -0.0035148 -0.0002280 9170 30.56 -17.079 -1.383 2006-03-30T00:07:29.260278272 INFO 2025-06-26 11:13:18,667 calibrate.py _nudge_pos():1806 [1] 493: 0.090 -0.0037228 -0.0019878 9585 31.95 -17.309 -11.530 2006-03-30T00:40:17.255461248 INFO 2025-06-26 11:13:19,242 calibrate.py _nudge_pos():1806 [1] 547: 0.100 -0.0000221 -0.0000227 15 0.05 -70.198 -90.309 2006-03-30T00:41:13.251625344 INFO 2025-06-26 11:13:19,327 calibrate.py _nudge_pos():1806 [1] 555: 0.100 -0.0082933 -0.0024666 13335 44.45 -27.717 -10.284 2006-03-30T01:25:47.258443136 INFO 2025-06-26 11:13:19,421 calibrate.py _nudge_pos():1806 [1] 564: 0.090 0.0000280 -0.0000270 25 0.08 51.971 -62.453 2006-03-30T01:26:00.257552640 INFO 2025-06-26 11:13:19,566 calibrate.py _nudge_pos():1806 [1] 577: 0.100 -0.0000681 0.0000142 30 0.10 -104.716 27.129 2006-03-30T01:26:18.256319744 INFO 2025-06-26 11:13:19,818 calibrate.py _nudge_pos():1806 [1] 601: 0.100 -0.0000300 -0.0000217 15 0.05 -95.598 -86.040 2006-03-30T01:26:44.254538752 INFO 2025-06-26 11:13:19,902 calibrate.py _nudge_pos():1806 [1] 609: 0.110 -0.0000522 -0.0000011 15 0.05 -166.308 -4.227 2006-03-30T01:26:54.253853824 INFO 2025-06-26 11:13:19,913 calibrate.py _nudge_pos():1806 [1] 610: 0.120 -0.0061890 -0.0014371 13435 44.78 -20.532 -5.947 2006-03-30T02:11:41.259781120 INFO 2025-06-26 11:13:20,381 calibrate.py _nudge_pos():1806 [1] 651: 0.110 -0.0000260 -0.0000404 55 0.18 -21.460 -41.544 2006-03-30T02:12:32.256287872 INFO 2025-06-26 11:13:20,413 calibrate.py _nudge_pos():1806 [1] 654: 0.130 -0.0059621 -0.0000428 13445 44.81 -19.766 -0.177 2006-03-30T02:57:23.251941888 INFO 2025-06-26 11:13:20,974 calibrate.py _nudge_pos():1806 [1] 706: 0.130 -0.0051504 0.0014907 8630 28.76 -26.604 9.603 2006-03-30T03:27:00.260208384 INFO 2025-06-26 11:13:21,568 calibrate.py _nudge_pos():1806 [1] 760: 0.130 -0.0012790 0.0003818 2760 9.20 -20.662 7.692 2006-03-30T03:37:05.258763264 INFO 2025-06-26 11:13:22,354 calibrate.py _nudge_pos():1806 [1] 834: 0.150 0.0016606 0.0049924 16165 53.88 4.579 17.169 2006-03-30T04:32:11.252287104 INFO 2025-06-26 11:13:23,103 calibrate.py _nudge_pos():1806 [1] 904: 0.140 -0.0000221 -0.0000105 15 0.05 -70.343 -41.521 2006-03-30T04:33:23.257354496 INFO 2025-06-26 11:13:23,191 calibrate.py _nudge_pos():1806 [1] 912: 0.160 0.0029430 0.0056211 16315 54.38 8.039 19.154 2006-03-30T05:27:53.253344256 INFO 2025-06-26 11:13:23,744 calibrate.py _nudge_pos():1806 [1] 962: 0.170 0.0045002 0.0054000 16405 54.68 12.224 18.300 2006-03-30T06:23:23.255223808 INFO 2025-06-26 11:13:24,506 calibrate.py _nudge_pos():1806 [1] 1031: 0.170 0.0050697 0.0032717 16160 53.86 13.979 11.255 2006-03-30T07:18:23.259157888 INFO 2025-06-26 11:13:25,160 calibrate.py _nudge_pos():1806 [1] 1091: 0.180 0.0052966 0.0040362 14878 49.61 15.856 15.075 2006-03-30T08:08:59.251178240 INFO 2025-06-26 11:13:25,725 calibrate.py _nudge_pos():1806 [1] 1143: 0.190 0.0043525 0.0034632 10815 36.05 17.931 17.803 2006-03-30T08:45:53.259508096 INFO 2025-06-26 11:13:26,326 calibrate.py _nudge_pos():1806 [1] 1198: 0.190 0.0022942 0.0033414 10890 36.30 9.386 17.058 2006-03-30T09:23:05.256605824 INFO 2025-06-26 11:13:26,943 calibrate.py _nudge_pos():1806 [1] 1254: 0.190 0.0010871 0.0046211 11575 38.58 4.184 22.195 2006-03-30T10:02:35.254250112 INFO 2025-06-26 11:13:27,555 calibrate.py _nudge_pos():1806 [1] 1310: 0.020 0.0021188 0.0061975 13046 43.48 7.234 26.410 2006-03-30T10:46:59.451740032 INFO 2025-06-26 11:13:28,130 calibrate.py _nudge_pos():1806 [1] 1362: 0.010 0.0031617 0.0044634 11745 39.15 11.990 21.128 2006-03-30T11:26:59.457328256 INFO 2025-06-26 11:13:28,748 calibrate.py _nudge_pos():1806 [1] 1418: 0.010 0.0031789 0.0034146 10764 35.88 13.152 17.635 2006-03-30T12:03:47.456069888 INFO 2025-06-26 11:13:29,461 calibrate.py _nudge_pos():1806 [1] 1483: 0.020 0.0039944 0.0029668 13240 44.13 13.435 12.457 2006-03-30T12:48:59.460284928 INFO 2025-06-26 11:13:30,103 calibrate.py _nudge_pos():1806 [1] 1541: 0.030 0.0017250 0.0007111 4755 15.85 16.157 8.316 2006-03-30T13:05:47.451232896 INFO 2025-06-26 11:13:30,699 calibrate.py _nudge_pos():1806 [1] 1595: 0.030 0.0034071 0.0024964 11465 38.21 13.232 12.105 2006-03-30T13:44:53.460520320 INFO 2025-06-26 11:13:31,398 calibrate.py _nudge_pos():1806 [1] 1655: 0.030 0.0014684 0.0023151 7835 26.11 8.345 16.428 2006-03-30T14:11:59.459131776 INFO 2025-06-26 11:13:32,008 calibrate.py _nudge_pos():1806 [1] 1709: 0.040 0.0016030 0.0033051 8735 29.11 8.170 21.036 2006-03-30T14:41:59.455823360 INFO 2025-06-26 11:13:34,914 calibrate.py _nudge_pos():1862 [1] 1950: - - - 2 0.00 - - INFO 2025-06-26 11:13:34,914 calibrate.py _nudge_pos():1868 [1] Points in final series = 337310 WARNING 2025-06-26 11:13:46,616 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 11.11 Hz INFO 2025-06-26 11:13:49,092 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:13:51,737 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:13:53,824 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:13:53,829 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2006.088.03/ctd1.nc INFO 2025-06-26 11:13:53,830 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd1_salinity values to NaN INFO 2025-06-26 11:13:53,831 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd1_salinity', Range(min=30, max=40))] INFO 2025-06-26 11:13:53,831 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 11:13:56,336 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:13:58,441 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 11:13:58,446 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2006.088.03/ctd2.nc INFO 2025-06-26 11:13:58,447 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd2_salinity values to NaN INFO 2025-06-26 11:13:58,448 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd2_salinity', Range(min=30, max=40))] INFO 2025-06-26 11:13:58,448 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 11:13:58,541 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 11:14:01,738 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 79680 81000 81840 83160 83520 84600 84900 85680 87180 87540 87900 193560 196260 307620 307800 310680 310860 311040 313800 315120 315480 425700 426300 479520 771360 1119960 1121340 1234020 1235340 1235580 1814880] INFO 2025-06-26 11:14:02,366 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 11:14:02,373 calibrate.py process_logs():3548 [1] Error processing biolume: missing variable "No variable named 'avg_biolume'. Variables on the dataset include ['time', 'rrr', 'cal_striing', 'pump', 'flow', 'humidity', 'temperature', 'time60hz', 'raw']" ERROR 2025-06-26 11:14:02,374 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.088.03 ERROR 2025-06-26 11:14:02,374 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2006.088.03 INFO 2025-06-26 11:14:02,630 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2006.088.03/dorado_2006.088.03_cal.nc INFO 2025-06-26 11:14:02,840 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_depth, biolume_flow, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, hs2_time, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time INFO 2025-06-26 11:14:02,844 process.py align():251 [1] Alignment steps for 2006.088.03 INFO 2025-06-26 11:14:02,885 align.py process_cal():139 [1] Processing dorado_2006.088.03_cal.nc from /data/auv_data/dorado/missionnetcdfs/2006.088.03 INFO 2025-06-26 11:14:02,984 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:14:02,993 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:14:03,237 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:14:03,251 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:14:03,488 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:14:03,500 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:14:03,643 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 11:14:03,643 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 11:14:03,738 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 11:14:03,751 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:14:03,980 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.088.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:14:03,990 align.py process_cal():249 [1] hs2_bbp470: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:14:04,188 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.088.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:14:04,198 align.py process_cal():249 [1] hs2_bbp676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:14:04,400 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2006.088.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=0.1397, y=-0.2794) INFO 2025-06-26 11:14:04,410 align.py process_cal():249 [1] hs2_fl676: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:14:04,606 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.088.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:14:04,616 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:14:04,823 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.088.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:14:04,833 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:14:05,030 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.088.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:14:05,040 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:14:05,247 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.088.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:14:05,256 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:14:05,457 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.088.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:14:05,467 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:14:05,667 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.088.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:14:05,676 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:14:05,878 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.088.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:14:05,889 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:14:06,092 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.088.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:14:06,102 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:14:06,305 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.088.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:14:06,315 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:14:06,515 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2006.088.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:14:06,524 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:14:06,724 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.088.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:14:06,735 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:14:06,937 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.088.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:14:06,947 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:14:07,151 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.088.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:14:07,164 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:14:07,366 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.088.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:14:07,376 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:14:07,578 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.088.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:14:07,588 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:14:07,786 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.088.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:14:07,797 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:14:08,004 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2006.088.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=1.003, y=0.0001) INFO 2025-06-26 11:14:08,014 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 11:14:08,268 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.68 INFO 2025-06-26 11:14:08,428 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.68 INFO 2025-06-26 11:14:08,589 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.68 INFO 2025-06-26 11:14:08,757 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 11:14:08,933 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 11:14:09,089 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2006.088.03/dorado_2006.088.03_align.nc INFO 2025-06-26 11:14:09,241 align.py write_netcdf():342 [1] Data variables written: biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp470, hs2_bbp676, hs2_depth, hs2_fl676, hs2_latitude, hs2_longitude, hs2_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, isus_temp, isus_time, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-06-26 11:14:09,243 process.py resample():273 [1] Resampling steps for 2006.088.03 INFO 2025-06-26 11:14:09,244 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 11:14:09,277 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.088.03/dorado_2006.088.03_align.nc mission netCDF file INFO 2025-06-26 11:14:09,285 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.088.03/dorado_2006.088.03_align.nc mission netCDF file INFO 2025-06-26 11:14:09,287 resample.py get_mission_start_end():1145 [1] navigation: 2006-03-29T20:01:38.870749056 to 2006-03-30T14:46:20.877914880 (0 days 00:00:00.019998592 before mission_end) INFO 2025-06-26 11:14:09,290 resample.py get_mission_start_end():1145 [1] hs2 : 2006-03-29T20:01:22.051901056 to 2006-03-30T14:46:20.897913472 (0 days 00:00:00 before mission_end) INFO 2025-06-26 11:14:09,293 resample.py get_mission_start_end():1145 [1] ctd1 : 2006-03-29T20:01:45.710280448 to 2006-03-30T14:46:20.737924608 (0 days 00:00:00.159988864 before mission_end) INFO 2025-06-26 11:14:09,295 resample.py get_mission_start_end():1145 [1] ctd2 : 2006-03-29T20:01:45.930265472 to 2006-03-30T14:46:20.717925760 (0 days 00:00:00.179987712 before mission_end) INFO 2025-06-26 11:14:09,297 resample.py get_mission_start_end():1145 [1] isus : 2006-03-29T20:02:43.726306176 to 2006-03-30T14:46:20.897913472 (0 days 00:00:00 before mission_end) INFO 2025-06-26 11:14:09,298 resample.py get_mission_start_end():1145 [1] biolume : 2006-03-29T20:01:16.922218368 to 2006-03-30T14:46:19.867949696 (0 days 00:00:01.029963776 before mission_end) INFO 2025-06-26 11:14:09,301 resample.py get_mission_start_end():1145 [1] tailcone : 2006-03-29T20:01:18.022177280 to 2006-03-30T14:46:20.797920512 (0 days 00:00:00.099992960 before mission_end) INFO 2025-06-26 11:14:09,302 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2006.088.03/dorado_2006.088.03_align.nc mission netCDF file INFO 2025-06-26 11:14:09,302 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:09,967 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:10,075 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:10,181 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:10,284 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:10,373 resample.py resample_variable():1031 [1] Resampling hs2_bbp470 with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:10,465 resample.py resample_variable():1031 [1] Resampling hs2_bbp676 with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:10,558 resample.py resample_variable():1031 [1] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:10,646 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:10,731 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:10,815 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:10,900 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:10,985 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:11,071 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:11,156 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:11,242 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:11,327 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:11,415 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:11,502 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:11,588 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:11,676 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:11,773 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:11,863 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:11,895 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:11,924 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:11,950 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:11,981 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:12,080 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 11:14:12,560 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2006.088.03/dorado_2006.088.03_1S.nc INFO 2025-06-26 11:14:14,844 create_products.py gulper_odv():401 [1] No gulper times found for 2006.088.03 INFO 2025-06-26 11:14:14,845 process.py archive():337 [1] Archiving steps for 2006.088.03 INFO 2025-06-26 11:14:14,845 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2006.088.03/dorado_2006.088.03, BASE_PATH = /data/auv_data INFO 2025-06-26 11:14:14,846 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2006.088.03/dorado_2006.088.03 files to /Volumes/AUVCTD/surveys/2006/netcdf INFO 2025-06-26 11:14:14,847 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.088.03_1S.nc INFO 2025-06-26 11:14:14,895 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.088.03/dorado_2006.088.03_1S.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:14:14,896 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.088.03_cal.nc INFO 2025-06-26 11:14:15,155 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.088.03/dorado_2006.088.03_cal.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:14:15,156 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2006/netcdf/dorado_2006.088.03_align.nc INFO 2025-06-26 11:14:15,390 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.088.03/dorado_2006.088.03_align.nc /Volumes/AUVCTD/surveys/2006/netcdf done. INFO 2025-06-26 11:14:15,456 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.088.03/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006088/2006.088.03 done. INFO 2025-06-26 11:14:15,531 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.088.03/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006088/2006.088.03 done. INFO 2025-06-26 11:14:15,536 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.088.03/gps.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006088/2006.088.03 done. INFO 2025-06-26 11:14:15,582 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.088.03/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006088/2006.088.03 done. INFO 2025-06-26 11:14:15,795 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.088.03/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006088/2006.088.03 done. INFO 2025-06-26 11:14:15,803 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.088.03/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006088/2006.088.03 done. INFO 2025-06-26 11:14:15,909 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.088.03/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006088/2006.088.03 done. INFO 2025-06-26 11:14:15,969 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.088.03/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006088/2006.088.03 done. INFO 2025-06-26 11:14:16,150 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.088.03/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2006/2006088/2006.088.03 done. INFO 2025-06-26 11:14:16,151 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 11:14:16,151 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2006.088.03/dorado_2006.088.03_processing.log /Volumes/AUVCTD/surveys/2006/netcdf